Overlap error using Rasterio mask in Python

Question

I have a satellite image raster file and a Shapefile consisting of several discrete polygons. I would like to individually extract (or mask) the Numpy image array for each of these polygons from the raster file.

Currently, I import the Shapefile using Fiona and create a list of the polygons. I have no problem masking the raster file using all the polygons at once. However when I try to use an individual polygon from the list I get an error: "ValueError: Input shapes do not overlap raster.". This is despite getting a successful result previously, and both files using the same CRS.

import rasterio
import shapefile
import fiona
import numpy as np

with fiona.open("test.shp", "r") as shapefile:

    features = [feature["geometry"] for feature in shapefile]

features = [x for x in features if x is not None]

This works:

with rasterio.open('sat_img_B01.jp2') as src:

    out_image, out_transform = rasterio.mask.mask(src, features,
                                                        crop=True)

This doesn't work (WindowError: windows do not intersect and ValueError: Input shapes do not overlap raster):

index = 0

with rasterio.open('sat_img_B01.jp2') as src:

    out_image, out_transform = rasterio.mask.mask(src, [features[index]], crop=True)

I guess I'm missing something fundamental! Is there an elegant way of extracting each polygon in the list 'features' as an individual image file/numpy array from the raster image?

Thanks!!

Firas Omrane · Accepted Answer · 2022-01-09 23:54:45Z

4

You have to make sure that both the shapefile and the raster image are using the same crs (Coordinate Reference System): try printing them.

edited Jan 9, 2022 at 23:54

answered Sep 2, 2019 at 21:28

Firas Omrane

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2 Comments

Claus Over a year ago

can you elaborate this point? I'm experiencing the same problem

Firas Omrane Over a year ago

@Claus I remember that my problem was that the shapefile and the raster image are not loaded with the same crs (coordinate reference system). I think that you already loaded both of them (shapefile using fiona) and (raster image using resterio). For the shapefile to print the crs using .crs property and for the resterio try to load the raster image using src = rasterio.open('image') and them print its crs src.crs. If the two crs are not the same the mask won't work. The solution is to change the crs of one of them to the other. I know this is late.

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